## Reading in : Callahan_1.CEL
## Reading in : Callahan_10.CEL
## Reading in : Callahan_11.CEL
## Reading in : Callahan_13.CEL
## Reading in : Callahan_14.CEL
## Reading in : Callahan_15.CEL
## Reading in : Callahan_16.CEL
## Reading in : Callahan_18.CEL
## Reading in : Callahan_19.CEL
## Reading in : Callahan_2.CEL
## Reading in : Callahan_20.CEL
## Reading in : Callahan_21.CEL
## Reading in : Callahan_22.CEL
## Reading in : Callahan_23.CEL
## Reading in : Callahan_24.CEL
## Reading in : Callahan_26.CEL
## Reading in : Callahan_27.CEL
## Reading in : Callahan_29.CEL
## Reading in : Callahan_3.CEL
## Reading in : Callahan_30.CEL
## Reading in : Callahan_31.CEL
## Reading in : Callahan_32.CEL
## Reading in : Callahan_33.CEL
## Reading in : Callahan_35.CEL
## Reading in : Callahan_36.CEL
## Reading in : Callahan_37.CEL
## Reading in : Callahan_38.CEL
## Reading in : Callahan_39.CEL
## Reading in : Callahan_4.CEL
## Reading in : Callahan_41.CEL
## Reading in : Callahan_42.CEL
## Reading in : Callahan_43.CEL
## Reading in : Callahan_44.CEL
## Reading in : Callahan_47.CEL
## Reading in : Callahan_48.CEL
## Reading in : Callahan_49.CEL
## Reading in : Callahan_50.CEL
## Reading in : Callahan_51.CEL
## Reading in : Callahan_52.CEL
## Reading in : Callahan_53.CEL
## Reading in : Callahan_6.CEL
## Reading in : Callahan_7.CEL
## Reading in : Callahan_8.CEL
## Raw data QC Plots ......
##  group :  Balb12wk

## group :  Balb3wkInv

## group :  Balb5wk

## group :  Balb6dPregnant

## group :  Balb7dLactation

## group :  FVB12wk

## group :  FVB12wkInv

## group :  FVB3wkInv

## group :  FVB5wk

## group :  FVB6dPregnant

## group :  FVB7dLactation

##   RLE and NUSE Plots ...
## 

##   Probset presence Plot ...
## 

## Post-Normalization plots ......
##  Background correcting
## Normalizing
## Calculating Expression
## group :  Balb12wk  after normalization

## group :  Balb3wkInv  after normalization

## group :  Balb5wk  after normalization

## group :  Balb6dPregnant  after normalization

## group :  Balb7dLactation  after normalization

## group :  FVB12wk  after normalization

## group :  FVB12wkInv  after normalization

## group :  FVB3wkInv  after normalization

## group :  FVB5wk  after normalization

## group :  FVB6dPregnant  after normalization

## group :  FVB7dLactation  after normalization

##   PCA and clustering plots ...
## 

## Limma, DEG and MAplot ......
## 

## DEG summary  ...
##                                adjPvalue<0.05 +abs(fc)>=1 +abs(fc)>=2
## Balb5wk-FVB5wk                           1030         244          46
## Balb12wk-FVB12wk                          473         167          40
## Balb6dPregnant-FVB6dPregnant              714         218          49
## Balb7dLactation-FVB7dLactation           2042         329          35
## Balb3wkInv-FVB3wkInv                      698         210          46
## FVB12wk-FVB5wk                            851         235          48
## FVB6dPregnant-FVB12wk                     731         191          15
## FVB7dLactation-FVB6dPregnant            18724        4023         576
## FVB3wkInv-FVB7dLactation                19392        4327         660
## Balb12wk-Balb5wk                           96          40           4
## Balb6dPregnant-Balb12wk                  1640         371          42
## Balb7dLactation-Balb6dPregnant          23243        5429         906
## Balb3wkInv-Balb7dLactation              21962        5004         764
## FVB12wkInv-FVB12wk                       1135         247          94
## FVB12wkInv-FVB3wkInv                      126          24           2
## [1] 0

End report.